[phenixbb] MR_Rosetta prerefine question

[Terwilliger, Thomas C]

Hi Heather,

Here is Frank DiMaio's quick reply:

Hi Tom,

There is no command line option but I can add code to do this.  I can get this checked in today (and can make a patch as well).

-Frank

So once Frank does this you can download a weekly-release of Rosetta and it should then be possible, or perhaps apply the patch that he mentions if you have a very recent release of Rosetta.  I'll let you know when it is available.

All the best,
Tom T

On Nov 8, 2013, at 11:37 AM, Heather L Condurso wrote:

Tom,

Thanks for the quick reply I will try #2 and see if that gives me a reasonable model.  If you hear from the Baker lab with a useful command please let me know.

Thanks again,
~Heather


On Fri, Nov 8, 2013 at 1:26 PM, Terwilliger, Thomas C <terwilliger at lanl.gov<mailto:terwilliger at lanl.gov>> wrote:
Hi Heather,

That would be useful, I can see that. I don't think there is an easy way to do that in mr_rosetta.   There are two possibilities I can think of.

1. You can pass any Rosetta commands you want to mr_rosetta with the keyword "rosetta_command".  I will ask Frank Dimaio from the Baker group about what commands might do this.

2. Alternatively you could fix it up by hand afterwards by using the phenix model tools to select some residues from the original model and some residues from the new model and then just make a composite PDB file.

All the best,
Tom T

On Nov 8, 2013, at 11:02 AM, Heather L Condurso wrote:

Dear all,

I am trying to use the rosetta prerefinement fuction of MR_rosetta to complete a homology model with missing stretches of amino acids.  Everything runs fine and residues are being added to fill the gaps using the fragment files, but rosetta is also altering parts of the model which should already be well placed.  Is there a way to tell Rosetta only to prerefine certain residues?

I've been following the command line suggestion:


phenix.mr_rosetta \
  seq_file=seq.dat \
  data=coords1.mtz \
  search_models=coords1.pdb \
  run_prerefine=True \
  number_of_prerefine_models=1000 \
  fragment_files = test3.gz \
  fragment_files = test9.gz \
  rescore_mr.relax=False \
  rosetta_models=100 \
  ncs_copies=2 \
  space_group=p212121  \
  use_all_plausible_sg=False \
  nproc=200 \
  group_run_command=qsub


Thanks,
Heather Condurso
condurso at bc.edu<mailto:condurso at bc.edu>
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